LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
  using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles

units		lj
atom_style	sphere
dimension	2

lattice		sq 0.5
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
region		box block 0 60 0 60 -0.5 0.5
create_box	2 box
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
  2 by 2 by 1 MPI processor grid
create_atoms	1 box
Created 3600 atoms
  create_atoms CPU = 0.001 seconds
change_box      all triclinic
Changing box ...
  triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)

# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
delete_atoms  region sphere1
Deleted 154 atoms, new total = 3446
delete_atoms  region sphere2
Deleted 158 atoms, new total = 3288
create_atoms 2 single 20.0 20.0 0.0 units box
Created 1 atoms
  create_atoms CPU = 0.000 seconds
create_atoms 2 single 60.0 60.0 0.0 units box
Created 1 atoms
  create_atoms CPU = 0.000 seconds

set		type 2 mass 400
Setting atom values ...
  2 settings made for mass
set		type 1 mass 1
Setting atom values ...
  3288 settings made for mass
set     type 2 diameter 20
Setting atom values ...
  2 settings made for diameter
set     type 1 diameter 1
Setting atom values ...
  3288 settings made for diameter

velocity	all create 1.44 87287 loop geom

# multi neighbor and comm for efficiency

neighbor	1 multi #multi/old
neigh_modify	delay 0 collection/interval 2 1 20
comm_modify     mode multi vel yes reduce/multi #multi/old

# colloid potential

pair_style      granular
pair_coeff      * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity

fix		1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix		2 all enforce2d
fix             3 all deform 1 xy erate 1e-3

#dump		1 all custom 1000 dump.granular id x y z radius

#dump		2 all image 1000 image.*.jpg type type #		zoom 1.5 center d 0.5 0.5 0.5
#dump_modify	2 pad 5 adiam 1 5.0 adiam 2 1.5

#dump		3 all movie 1000 movie.mpg type type #		zoom 1.5 center d 0.5 0.5 0.5
#dump_modify	3 pad 5 adiam 1 5.0 adiam 2 1.5

thermo_style	custom step temp epair etotal press vol
thermo		1000

timestep	0.005

run		50000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 21
  ghost atom cutoff = 21
  binsize = 1, bins = 85 85 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair granular, perpetual
      attributes: half, newton on, size, history
      pair build: half/size/multi/newton/tri
      stencil: half/multi/2d/tri
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 10.09 | 10.10 | 10.10 Mbytes
Step Temp E_pair TotEng Press Volume 
       0         1.44            0    1.4395623   0.66837658         7200 
    1000   0.32605303            0   0.32595393   0.17341558    7862.5037 
    2000   0.12631567            0   0.12627728  0.069188881    8216.7174 
    3000  0.069373812            0  0.069352726  0.040740832    8344.2982 
    4000  0.045084633            0  0.045070929  0.029328609    8239.3656 
    5000  0.032681746            0  0.032671813  0.025416741    7943.7831 
    6000  0.026301239            0  0.026293245  0.021418793    7617.8426 
    7000  0.021666723            0  0.021660138  0.018961011    7255.9338 
    8000  0.018141337            0  0.018135823  0.019306113    6887.4963 
    9000  0.015922309            0  0.015917469  0.020033398     6524.016 
   10000  0.014744547            0  0.014740066  0.020959503    6168.1945 
   11000  0.013872852            0  0.013868636  0.021708943    5823.3153 
   12000  0.013321594            0  0.013317545   0.02332141    5491.4979 
   13000   0.01269964            0  0.012695779  0.024796428    5174.6263 
   14000   0.01227055            0  0.012266821  0.027785072    4873.4516 
   15000  0.012120508            0  0.012116824  0.029656636    4588.8603 
   16000  0.011612027            0  0.011608498  0.034695109    4320.4674 
   17000  0.011216697            0  0.011213288  0.042746966    4069.4275 
   18000  0.010950166            0  0.010946838  0.053528994    3835.5439 
   19000  0.010887635            0  0.010884325  0.069684492     3619.562 
   20000  0.010563449            0  0.010560238   0.08654561    3420.2636 
   21000 0.0092336323            0 0.0092308257   0.11286068    3237.1408 
   22000  0.006929086            0 0.0069269799   0.15018917    3072.0438 
   23000 0.0052239156            0 0.0052223277   0.19067193     2924.441 
   24000 0.0044210081            0 0.0044196644   0.23908686    2793.2426 
   25000 0.0034916086            0 0.0034905473   0.29112824    2678.7912 
   26000  0.002549072            0 0.0025482972   0.33567824    2579.3738 
   27000 0.0020890726            0 0.0020884377   0.37328514    2491.0502 
   28000  0.001772982            0 0.0017724431   0.41079958    2411.9111 
   29000  0.001127719            0 0.0011273762   0.44752241    2341.1888 
   30000 0.00053266563            0 0.00053250373   0.48791815    2278.5611 
   31000 0.00050278646            0 0.00050263364   0.52896525    2224.5328 
   32000 0.00051880956            0 0.00051865187   0.56884574    2178.6674 
   33000 0.00054908167            0 0.00054891477    0.6016387    2140.3696 
   34000 0.00075213884            0 0.00075191023   0.62070188    2106.6504 
   35000 0.00081295162            0 0.00081270452   0.63492031    2073.0077 
   36000 0.00056699821            0 0.00056682587   0.65608409    2038.3251 
   37000 0.0003540723            0 0.00035396468   0.68803919     2005.497 
   38000 0.00031139738            0 0.00031130273   0.72103717    1977.7345 
   39000 0.00034087822            0 0.00034077461   0.74697975    1954.8979 
   40000 0.00035452426            0 0.0003544165   0.76682035    1934.5695 
   41000 0.00030882258            0 0.00030872871   0.78390763    1914.3326 
   42000 0.00025492799            0 0.00025485051   0.80439795    1893.1474 
   43000 0.00021545017            0 0.00021538468   0.82803644     1872.073 
   44000 0.00017293257            0   0.00017288   0.85436769    1852.6548 
   45000 0.00014097725            0 0.0001409344    0.8796181    1836.0087 
   46000 0.0001139199            0 0.00011388527   0.90006173    1821.7977 
   47000 0.00012678598            0 0.00012674745   0.90876359    1808.4913 
   48000 0.00013796773            0 0.00013792579   0.93661523    1793.8082 
   49000 0.00014723144            0 0.00014718669   0.95869417    1779.1875 
   50000 0.00013610653            0 0.00013606516   0.97777198    1765.3247 
Loop time of 17.7405 on 4 procs for 50000 steps with 3290 atoms

Performance: 1217551.996 tau/day, 2818.407 timesteps/s
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 6.6629     | 9.6168     | 12.444     |  76.6 | 54.21
Neigh   | 0.049771   | 0.055182   | 0.06133    |   2.0 |  0.31
Comm    | 1.7883     | 4.6306     | 7.6179     | 111.5 | 26.10
Output  | 0.00085342 | 0.0010606  | 0.0015425  |   0.9 |  0.01
Modify  | 2.7244     | 2.895      | 3.0436     |   8.2 | 16.32
Other   |            | 0.5419     |            |       |  3.05

Nlocal:        822.500 ave         897 max         779 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Nghost:        190.500 ave         211 max         179 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs:        6665.75 ave        7329 max        6104 min
Histogram: 1 0 0 1 1 0 0 0 0 1

Total # of neighbors = 26663
Ave neighs/atom = 8.1042553
Neighbor list builds = 342
Dangerous builds = 0

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:17
